Merge remote-tracking branch 'origin/r3.2.0'

README.md

@@ -1,10 +1,10 @@
-# Jenetics (_3.1.0_)
+# Jenetics (_3.2.0_)
 
 **Jenetics** is an **Genetic Algorithm**, respectively an **Evolutionary Algorithm**, library written in Java. It is designed with a clear separation of the several concepts of the algorithm, e.g. `Gene`, `Chromosome`, `Genotype`, `Phenotype`, `Population` and fitness `Function`. **Jenetics** allows you to minimize and maximize the given fitness function without tweaking it. In contrast to other GA implementations, the library uses the concept of an evolution stream (`EvolutionStream`) for executing the evolution steps. Since the `EvolutionStream` implements the Java Stream interface, it works smoothly with the rest of the Java Stream API.
 
 ## Documentation
 
-The library is fully documented ([javadoc](http://jenetics.io/javadoc/org.jenetics/index.html)) and comes with an user manual ([pdf](http://jenetics.io/manual/manual-3.1.0.pdf)).
+The library is fully documented ([javadoc](http://jenetics.io/javadoc/org.jenetics/3.2/index.html)) and comes with an user manual ([pdf](http://jenetics.io/manual/manual-3.2.0.pdf)).
 
 
 ## Requirements
@@ -17,19 +17,19 @@ The library is fully documented ([javadoc](http://jenetics.io/javadoc/org.jeneti
 *  **Gradle 2.x**: [Gradle](http://www.gradle.org/) is used for building the library. (Gradle is download automatically, if you are using the Gradle Wrapper script `gradlew`, located in the base directory, for building the library.)
 
 ### Test compile/execution
-*  **TestNG 8.8**: Jenetics uses [TestNG](http://testng.org/doc/index.html) framework for unit tests.
-*  **Apache Commons Math 3.4.1**: [Library](http://commons.apache.org/proper/commons-math/) is used for testing statistical collectors.
+*  **TestNG 6.9.4**: Jenetics uses [TestNG](http://testng.org/doc/index.html) framework for unit tests.
+*  **Apache Commons Math 3.5**: [Library](http://commons.apache.org/proper/commons-math/) is used for testing statistical collectors.
 
 ## Download
-* **Github**: <https://github.com/jenetics/jenetics/releases/download/v3.1.0/jenetics-3.1.0.zip>
+* **Github**: <https://github.com/jenetics/jenetics/releases/download/v3.2.0/jenetics-3.2.0.zip>
 *  **Sourceforge**:  <https://sourceforge.net/projects/jenetics/files/latest/download>
-*  **Maven**: `org.bitbucket.fwilhelm:org.jenetics:3.1.0` on [Maven Central](http://search.maven.org/#search|ga|1|a%3A%22org.jenetics%22)
+*  **Maven**: `org.bitbucket.fwilhelm:org.jenetics:3.2.0` on [Maven Central](http://search.maven.org/#search|ga|1|a%3A%22org.jenetics%22)
 
 ## Build Jenetics
 
 [![Build Status](https://travis-ci.org/jenetics/jenetics.svg?branch=master)](https://travis-ci.org/jenetics/jenetics)
 
-For building the Jenetics library from source, download the most recent, stable package version from [Github](https://github.com/jenetics/jenetics/releases/download/v3.1.0/jenetics-3.1.0.zip) (or [Sourceforge](https://sourceforge.net/projects/jenetics/files/latest/download)) and extract it to some build directory.
+For building the Jenetics library from source, download the most recent, stable package version from [Github](https://github.com/jenetics/jenetics/releases/download/v3.2.0/jenetics-3.2.0.zip) (or [Sourceforge](https://sourceforge.net/projects/jenetics/files/latest/download)) and extract it to some build directory.
 
     $ unzip jenetics-<version>.zip -d <builddir>
 
@@ -71,7 +71,7 @@ The latest Eclipse version (4.4.2) has problems compiling some _valid_ lambda ex
          .builder((Function<Genotype<BitGene>, Integer>)HelloWorld::eval, gtf)
          .build();
 
- Or you are using [IntelliJ 14](https://www.jetbrains.com/idea/download/) instead.
+ Or you are using ![IntelliJ 14](https://www.jetbrains.com/idea/download/) instead.
 
 ## Example
 
@@ -142,6 +142,23 @@ The library is licensed under the [Apache License, Version 2.0](http://www.apach
 
 ## Release notes
 
+### 3.2.0
+
+#### Improvements
+
+* [#24](https://github.com/jenetics/jenetics/issues/24): Stabilize statistical selector tests.
+* [#25](https://github.com/jenetics/jenetics/issues/25): Remove `testng.xml` file. The test classes are now determined automatically.
+* [#40](https://github.com/jenetics/jenetics/issues/40): Introduce `Codec` interface for defining problem encodings.
+* Add _Internal_ section in manual, which describes implementation details.
+
+#### Bug fixes
+
+* [#33](https://github.com/jenetics/jenetics/issues/33): Selectors must not change the input population. This occasionally caused `ConcurrentModificationException`.  Such selectors are now creating a defensive copy of the input population.
+* [#34](https://github.com/jenetics/jenetics/issues/34): `IndexOutOfBoundsException` when selecting populations which are too short.
+* [#35](https://github.com/jenetics/jenetics/issues/35): `IndexOutOfBoundsException` when altering populations which are too short.
+* [#39](https://github.com/jenetics/jenetics/issues/39): Numerical instabilities of `ProbabilitySelector`.
+* [#47](https://github.com/jenetics/jenetics/issues/47): `Engine` deadlock for long running fitness functions.
+
 ### 3.1.0
 
 #### Improvements
@@ -165,3 +182,7 @@ The library is licensed under the [Apache License, Version 2.0](http://www.apach
 
 * Rewrite of *engine* classes to make use of Java 8 Stream API.
 
+## Used software
+
+<a href="https://www.jetbrains.com/idea/">![IntelliJ](https://www.jetbrains.com/idea/docs/logo_intellij_idea.png)</a>
+

build.gradle

@@ -73,7 +73,7 @@ allprojects { Project prj ->
 }
 
 task wrapper(type: Wrapper) {
-	gradleVersion = '2.3'
+	gradleVersion = '2.4'
 }
 
 task trimLineFeed(type: TrimLineFeedTask) {

buildSrc/src/main/groovy/org/jenetics/gradle/plugin/LyxPlugin.groovy

@@ -21,6 +21,7 @@ package org.jenetics.gradle.plugin
 
 import org.apache.tools.ant.filters.ReplaceTokens
 import org.gradle.api.Project
+import org.jenetics.gradle.Version
 import org.jenetics.gradle.task.Lyx2PDFTask
 
 /**
@@ -56,7 +57,10 @@ class LyxPlugin extends JeneticsPlugin {
 				into project.build.temporaryDir
 				filter(ReplaceTokens, tokens: [
 					__year__: project.copyrightYear,
-					__identifier__: project.manualIdentifier
+					__identifier__: project.manualIdentifier,
+					__version__: project.version,
+					__minor_version__: Version.parse(project.version.toString())
+						.minorVersionString()
 				])
 			}
 			copy {

buildSrc/src/main/groovy/org/jenetics/gradle/plugin/SetupPlugin.groovy

@@ -112,13 +112,10 @@ class SetupPlugin extends JeneticsPlugin {
 	private void configureTestReporting() {
 		plugins.apply(JacocoPlugin)
 		project.test {
+			outputs.upToDateWhen { false }
 			useTestNG {
-				//parallel = 'tests' // 'methods'
-				//threadCount = Runtime.runtime.availableProcessors() + 1
-				//include '**/*Test.class'
-				suites project.file(
-                        "${project.projectDir}/src/test/resources/testng.xml"
-                    )
+				parallel = 'tests' // 'methods'
+				threadCount = Runtime.runtime.availableProcessors() + 1
 			}
 		}
 

buildSrc/src/main/java/org/jenetics/gradle/Version.java

@@ -100,6 +100,18 @@ public int compareTo(final Version version) {
 		return comp;
 	}
 
+	public String majorVersionString() {
+		return Integer.toString(_major);
+	}
+
+	public String minorVersionString() {
+		return format("%d.%d", _major, _minor);
+	}
+
+	public String microVersionString() {
+		return format("%d.%d.%d", _major, _minor, _micro);
+	}
+
 	@Override
 	public int hashCode() {
 		int hash = getClass().hashCode();

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
-#Sun Apr 19 21:26:59 CEST 2015
+#Thu May 21 19:03:17 CEST 2015
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-2.3-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-2.4-bin.zip

include.properties

@@ -1,6 +1,6 @@
 # Definition of the external projects.
-Include.Apache.Commons.Math=org.apache.commons:commons-math3:3.4.1
+Include.Apache.Commons.Math=org.apache.commons:commons-math3:3.5
 Include.Jettison=org.codehaus.jettison:jettison:1.4.1
-Include.JMH.Core=org.openjdk.jmh:jmh-core:1.8
-Include.JMH.Processor=org.openjdk.jmh:jmh-generator-annprocess:1.8
-Include.TestNG=org.testng:testng:6.8.21
+Include.JMH.Core=org.openjdk.jmh:jmh-core:1.10.1
+Include.JMH.Processor=org.openjdk.jmh:jmh-generator-annprocess:1.10.1
+Include.TestNG=org.testng:testng:6.9.4